AdmiralenOla Scoary issues

AdmiralenOla / Scoary

Pan-genome wide association studies

GNU General Public License v3.0

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issues

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depends on deprecated pkg_resources module

#112 emollier opened 2 weeks ago
0
ete3 does not need six anymore for a long time

#111 a-detiste opened 2 months ago
0
Migrate to SciPy 1.12.0.

#110 emollier opened 5 months ago
0
missing data in genotype file

#109 snackens opened 1 year ago
0
Significance of the worst_pairwise_p

#108 plasmid02 opened 1 year ago
3
UnicodeDecode Error while reading traits file

#107 arijitnus opened 1 year ago
0
fix ValueError: invalid mode: 'rU' with python3.11

#106 emollier opened 1 year ago
1
Unrecognized character found in trait file

#105 shaodongyan opened 1 year ago
2
Should assemblies be removed if core gene alignment shows redundancies?

#104 chahatupreti opened 2 years ago
0
Stop at "Calculating max number of contrasting pairs for each nominally significant gene: in the Ternimal

#103 Xiangyang1984 opened 2 years ago
0
How to generate manhatton plot from Scoary results

#102 sekhwal closed 2 years ago
1
genetic differences among populations defined by population analysis

#101 kopelol closed 2 years ago
2
How can I explore the differences between subpopulations defined using population analysis?

#100 kopelol closed 2 years ago
0
Large number of significant genes

#99 LeonardosMageiros closed 2 years ago
1
Convert vcf from parsnp to Scoary input

#98 nicola-palmieri opened 2 years ago
0
Startcol error

#97 GillNdhlovu opened 2 years ago
1
Support for non-binary traits

#96 MrTomRod opened 2 years ago
9
collapse flag output

#95 jayvorn opened 3 years ago
0
Question about --collapse

#94 Antonia-Chalka opened 3 years ago
2
I got the CSV files of all trait related genes. How do I get the important genes in all trait files?

#93 971202 opened 3 years ago
0
/var/spool/gridengine/execd/cu17/job_scripts/371921: line 11: 9884 Killed

#92 971202 closed 3 years ago
1
Gene enrichments across host sites

#91 spatz018 opened 3 years ago
0
IndexError: list index out of range

#90 hollygene opened 3 years ago
4
_csv.Error: field larger than field limit (131072)

#89 ga23981 opened 3 years ago
0
Scoary output for phandango

#88 pavlo888 opened 3 years ago
1
Separate trait files

#87 zakisaati closed 3 years ago
1
gene_presence_absence.csv file from Roary

#86 haruosuz closed 4 years ago
1
Self created absence_presence file as input?

#85 maesaar closed 4 years ago
2
Missing genes in results

#84 jimmyliu1326 closed 4 years ago
1
Scoary run in cluster MPI???

#83 germant13 opened 4 years ago
1
How to filter Scoary Results

#82 noahaus closed 4 years ago
2
Empty output files with k-mer GWAS

#81 npavlovikj closed 4 years ago
1
Scoary not accepting my traits.csv

#80 bkm23644 closed 4 years ago
1
Splitting paralogs influence to Scoary?

#79 nbawe closed 4 years ago
2
Piggy output as input to use with Scoary?

#78 maesaar closed 4 years ago
3
error

#77 darwinbandoy closed 4 years ago
9
VCF GWAS

#76 ahmedmagds closed 4 years ago
2
Add functionality to handle missing values in the genetic data

#75 AdmiralenOla opened 5 years ago
0
Please switch to Python3

#74 tillea opened 5 years ago
0
Test data are missing so test suite does not succeed

#73 tillea opened 5 years ago
0
Don't crash when newick file has node labels

#72 AdmiralenOla opened 5 years ago
2
Segentation fault

#71 giggzie02 closed 5 years ago
1
How to output information concerning all genes ?

#70 mylanhong closed 5 years ago
1
RuntimeError: maximum recursion depth exceeded while calling a Python object

#69 mlaziz opened 6 years ago
4
GenomeIDs not matching custom tree and gene pres/abs

#68 moorembioinfo closed 6 years ago
2
Not all genes are reported with "-p 1.0"

#67 IEkAdN closed 6 years ago
2
Incomplete presence/absence data from Single-cell genomes

#66 thackl opened 6 years ago
3
SNP gwas

#65 samlipworth closed 6 years ago
2
Genomic associations between subspecies

#64 karchern closed 7 years ago
4
Changes to vcf2scoary

#63 AdmiralenOla closed 7 years ago
0